OHSU_TMT_Publications

List of publications where TMT labeling was used in the OHSU PSR core. Many papers use the freely available PAW pipeline. Several of the studies used multiple TMT-plexes and the IRS method to extend isobaric labeling to larger numbers of samples.

The recommended reference to cite for internal reference scaling is Plubell, et al., MCP 2017 (Reference 3 below).

Some work from other laboratories and institutions using methods/techniques developed in the OHSU proteomic core is also listed.

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OHSU Work (chronological)

1. Huan, J., Hornick, N.I., Goloviznina, N.A., Kamimae-Lanning, A.N., David, L.L., Wilmarth, P.A., Mori, T., Chevillet, J.R., Narla, A., Roberts, C.T. and Loriaux, M.M., 2015. Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes. Leukemia, 29(12), pp.2285-2295.

2. Midgett, M., López, C.S., David, L., Maloyan, A. and Rugonyi, S., 2017. Increased hemodynamic load in early embryonic stages alters endocardial to mesenchymal transition. Frontiers in physiology, 8, p.56.

3. Plubell, D.L., Wilmarth, P.A., Zhao, Y., Fenton, A.M., Minnier, J., Reddy, A.P., Klimek, J., Yang, X., David, L.L. and Pamir, N., 2017. Extended multiplexing of tandem mass tags (TMT) labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Molecular & Cellular Proteomics, 16(5), pp.873-890.

4. Whitson, J.A., Wilmarth, P.A., Klimek, J., Monnier, V.M., David, L. and Fan, X., 2017. Proteomic analysis of the glutathione-deficient LEGSKO mouse lens reveals activation of EMT signaling, loss of lens specific markers, and changes in stress response proteins. Free Radical Biology and Medicine, 113, pp.84-96.

5. Krey, J.F., Dumont, R.A., Wilmarth, P.A., David, L.L., Johnson, K.R. and Barr-Gillespie, P.G., 2018. ELMOD1 stimulates ARF6-GTP hydrolysis to stabilize apical structures in developing vestibular hair cells. Journal of Neuroscience, 38(4), pp.843-857.

6. Vranka, J.A., Staverosky, J.A., Reddy, A.P., Wilmarth, P.A., David, L.L., Acott, T.S., Russell, P. and Raghunathan, V.K., 2018. Biomechanical rigidity and quantitative proteomics analysis of segmental regions of the trabecular meshwork at physiologic and elevated pressures. Investigative ophthalmology & visual science, 59(1), pp.246-259.

7. Hulett, T.W., Jensen, S.M., Wilmarth, P.A., Reddy, A.P., Ballesteros-Merino, C., Afentoulis, M.E., Dubay, C., David, L.L. and Fox, B.A., 2018. Coordinated responses to individual tumor antigens by IgG antibody and CD8+ T cells following cancer vaccination. Journal for immunotherapy of cancer, 6(1), p.27.

8. Plubell, D.L., Fenton, A.M., Wilmarth, P.A., Bergstrom, P., Zhao, Y., Minnier, J., Heinecke, J.W., Yang, X. and Pamir, N., 2018. GM-CSF driven myeloid cells in adipose tissue link weight gain and insulin resistance via formation of 2-aminoadipate. Scientific reports, 8(1), pp.1-12.

9. Hegarty, D.M., David, L.L. and Aicher, S.A., 2018. Lacrimal gland denervation alters tear protein composition and impairs ipsilateral eye closures and corneal nociception. Investigative ophthalmology & visual science, 59(12), pp.5217-5224.

10. Wakasaki, R., Matsushita, K., Golgotiu, K., Anderson, S., Eiwaz, M.B., Orton, D.J., Han, S.J., Lee, H.T., Smith, R.D., Rodland, K.D., Piehowski, P.D. and Hutchens, M.P., 2019. Glomerular filtrate proteins in acute cardiorenal syndrome. JCI insight, 4(4).

11. Wakeham, C.M., Wilmarth, P.A., Cunliffe, J.M., Klimek, J.E., Ren, G., David, L.L. and Morgans, C.W., 2019. Identification of PKCα-dependent phosphoproteins in mouse retina. Journal of proteomics, 206, p.103423.

12. Rocheleau, A.D., Melrose, A.R., Cunliffe, J.M., Klimek, J., Babur, Ö., Tassi Yunga, S., Ngo, A.T., Pang, J., David, L.L., McCarty, O.J. and Aslan, J.E., 2019. Identification, Quantification, and System Analysis of Protein N‐ε Lysine Methylation in Anucleate Blood Platelets. Proteomics, 19(11), p.1900001.

13. Abdelhamed, S., Butler, J.T., Doron, B., Halse, A., Nemecek, E., Wilmarth, P.A., Marks, D.L., Chang, B.H., Horton, T. and Kurre, P., 2019. Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche. EMBO reports, 20(7), p.e47546.

14. Cheung, C.Y., Anderson, D.F. and Brace, R.A., 2019. Multiomics analyses of vesicular transport pathway-specific transcripts and proteins in ovine amnion: responses to altered intramembranous transport. Physiological genomics, 51(7), pp.267-278.

15. Svensson, K., LaBarge, S.A., Sathe, A., Martins, V.F., Tahvilian, S., Cunliffe, J.M., Sasik, R., Mahata, S.K., Meyer, G.A., Philp, A., David, L.L., Ward, S.R., McCurdy, C.E., Aslan, J.E. and Schenk, S., 2020. p300 and cAMP response element‐binding protein‐binding protein in skeletal muscle homeostasis, contractile function, and survival. Journal of cachexia, sarcopenia and muscle, 11(2), pp.464-477.

16. Cheung, C.Y. and Brace, R.A., 2020. Altered proteomics profile in the amnion of patients with oligohydramnios. Physiological reports, 8(4), p.e14381.

17. Hernandez, F., Luther, S., Aryal, S., Weatherbee, B.A., Siddam, A.D., Reddy, A.P., Wilmarth, P., David, L., Gautier-Courteille, C., Paillard, L. and Lachke, S.A., 2020. Celf1 regulates the small heat shock protein Hspb8 in lens development. Investigative Ophthalmology & Visual Science, 61(7), pp.2870-2870.

18. Özgün Babur, Alexander Melrose, Jennifer Cunliffe, John Klimek, Jiaqing Pang, Anna-Liisa Sepp, Jevgenia Zilberman-Rudenko, Samuel Tassi Yunga, Tony Zheng, Iván Parra-Izquierdo, Jessica Minnier, Owen McCarty, Emek Demir, Ashok Reddy, Phillip Wilmarth, Larry L David, Joseph E Aslan; 2020. Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. Blood, 136(20), pp.2346-2358.

19. Chatterjee, N., Fraile-Bethencourt, E., Baris, A., Espinosa-Diez, C. and Anand, S., 2021. MicroRNA-494 regulates Endoplasmic Reticulum stress in endothelial cells. Frontiers in Cell and Developmental Biology, 9, p.1846.

20. Han, L., Park, D., Reddy, A., Wilmarth, P.A. and Jensen, J.T., 2021. Comparing endocervical mucus proteome of humans and rhesus macaques. PROTEOMICS–Clinical Applications, p.2100023..

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Other Institutions (reverse chronological):

1. Birk, M.S., Ahmed-Begrich, R., Tran, S., Elsholz, A.K., Frese, C.K. and Charpentier, E., 2021. Time-Resolved Proteome Analysis of Listeria monocytogenes during Infection Reveals the Role of the AAA+ Chaperone ClpC for Host Cell Adaptation. Msystems, 6(4), pp.e00215-21.

2. Pandya, N.J., Wang, C., Costa, V., Lopatta, P., Meier, S., Zampeta, F.I., Punt, A.M., Mientjes, E., Grossen, P., Distler, T. and Tzouros, M., 2021. Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology. Cell Reports Medicine, 2(8), p.100360.

3. Li, S., Li, X., Yang, S., Pi, H., Li, Z., Yao, P., Zhang, Q., Wang, Q., Shen, P., Li, X. and Ji, J., 2021. Proteomic landscape of exosomes reveals the functional contributions of CD151 in triple-negative breast cancer. Molecular & Cellular Proteomics, 20.

4. Min, C.W., Gupta, R., Truong, N.V., Bae, J.W., Ko, J.M., Lee, B.W. and Kim, S.T., 2020. A TMT-based quantitative proteomic analysis provides insights into the protein changes in the seeds of high-and low-protein content soybean cultivars. Journal of Plant Biotechnology, 47(3), pp.209-217.

5. Cao, X., Lilla, S., Cao, Z., Pringle, M.A., Oka, O.B., Robinson, P.J., Szmaja, T., Van Lith, M., Zanivan, S. and Bulleid, N.J., 2020. The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins. Journal of cell science, 133(8).

6. Khan, M.J., Desaire, H., Lopez, O.L., Kamboh, M.I. and Robinson, R.A., 2021. Why Inclusion Matters for Alzheimer’s Disease Biomarker Discovery in Plasma. Journal of Alzheimer's Disease, 1 Jan. 2021:1327-1344.

7. Khan, M.J., Desaire, H., Lopez, O.L., Kamboh, M.I. and Robinson, R.A., 2021. Dataset of why inclusion matters for Alzheimer's disease biomarker discovery in plasma. Data in brief, 35, p.106923.

8. Zaini, P.A., Feinberg, N.G., Grilo, F.S., Saxe, H.J., Salemi, M.R., Phinney, B.S., Crisosto, C.H. and Dandekar, A.M., 2020. Comparative Proteomic Analysis of Walnut (Juglans regia L.) Pellicle Tissues Reveals the Regulation of Nut Quality Attributes. Life, 10(12), p.314.

9. HD Sagawa, C., de AB Assis, R., Zaini, P.A., Wilmarth, P.A., Phinney, B.S., Moreira, L.M. and Dandekar, A.M., 2020. Proteome Analysis of Walnut Bacterial Blight Disease. International Journal of Molecular Sciences, 21(20), p.7453.

10. Doud, E.H., Shetty, T., Abt, M., Mosley, A.L., Corson, T.W., Mehta, A. and Yeh, E.S., 2020. NF-κB Signaling Is Regulated by Fucosylation in Metastatic Breast Cancer Cells. Biomedicines, 8(12), p.600.

11. López-Janeiro, Á., Ruz-Caracuel, I., Ramón-Patino, J.L., Los Ríos, D., De Los, V., Villalba Esparza, M.V., Berjón, A., Yébenes, L., Hernández, A., Masetto, I. and Kadioglu, E., 2021. Proteomic Analysis of Low-Grade, Early-Stage Endometrial Carcinoma Reveals New Dysregulated Pathways Associated with Cell Death and Cell Signaling. Cancers, 13(4), p.794.

12. Chen, S.K., Wang, Y.C., Lin, T.Y., Wu, H.J., Huang, C.J. and Ku, W.C., 2021. G-Protein-coupled Estrogen Receptor 1 Agonist G-1 Perturbs Sunitinib Resistance-related Phosphoproteomic Signatures in Renal Cell Carcinoma. Cancer Genomics & Proteomics, 18(3), pp.207-220.

13. Brenes, A.J., Yoshikawa, H., Bensaddek, D., Mirauta, B., Seaton, D., Hukelmann, J.L., Jiang, H., Stegle, O. and Lamond, A.I., 2021. Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome. Cell Reports, 35(4), p.109032.

14. Apel, F., Andreeva, L., Knackstedt, L.S., Streeck, R., Frese, C.K., Goosmann, C., Hopfner, K.P. and Zychlinsky, A., 2021. The cytosolic DNA sensor cGAS recognizes neutrophil extracellular traps. Science Signaling, 14(673).

15. Courtland, J.L., Bradshaw, T.W., Waitt, G., Soderblom, E.J., Ho, T., Rajab, A., Vancini, R., Kim, I.H. and Soderling, S.H., 2021. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. Elife, 10, p.e61590.

16. King, C.D. and Robinson, R.A., 2020. Evaluating Combined Precursor Isotopic Labeling and Isobaric Tagging Performance on Orbitraps To Study the Peripheral Proteome of Alzheimer’s Disease. Analytical chemistry, 92(4), pp.2911-2916.

17. Cao, X., Lilla, S., Cao, Z., Pringle, M.A., Oka, O.B., Robinson, P.J., Szmaja, T., Van Lith, M., Zanivan, S. and Bulleid, N.J., 2020. The mammalian cytosolic thioredoxin reductase pathway acts via a membrane protein to reduce ER-localised proteins. Journal of cell science, 133(8). - Uses MaxQuant and IRS; MS2 Fusion Lumos; Thioredoxin reductase pathway study

18. Contreras-Llano, L.E., Meyer, C., Liu, Y., Sarker, M., Lim, S., Longo, M.L. and Tan, C., 2020. Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits. Nature communications, 11(1), pp.1-10. - Uses PAW pipeline and IRS; SPS-MS3 Fusion Lumos; E. coli engineering

19. Min, C.W., Hyeon, H., Gupta, R., Park, J., Cheon, Y.E., Lee, G.H., Jang, J.W., Ryu, H.W., Lee, B.W., Park, S.U. and Kim, Y., 2020. Integrated proteomics and metabolomics analysis highlights correlative metabolite-protein networks in soybean seeds subjected to warm-water soaking. Journal of Agricultural and Food Chemistry, 68(30), pp.8057-8067.

20. Min, C.W., Park, J., Bae, J.W., Agrawal, G.K., Rakwal, R., Kim, Y., Yang, P., Kim, S.T. and Gupta, R., 2020. In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis. Cells, 9(6), p.1517. - MaxQuant and IRS; MS2 Q Exactive; Soybean seed Proteomics

21. Amin, B. and Robinson, R.A., 2020. Dataset of quantitative proteomic analysis to understand aging processes in rabbit liver. Data in Brief, p.105701. - Proteome Discoverer and IRS; SPS-MS3 Fusion Lumos; Aging changes in rabbit liver

22. Amin, B., Ford, K.I. and Robinson, R.A., 2020. Quantitative proteomics to study aging in rabbit liver. Mechanisms of Ageing and Development, p.111227. - Proteome Discoverer and IRS; SPS-MS3 Fusion Lumos; Aging changes in rabbit liver

23. Bojkova, D., Klann, K., Koch, B. et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature (2020). https://doi.org/10.1038/s41586-020-2332-7 - Proteome Discoverer/SEQUEST and IRS; MS2 Q Exactive HF; SARS-CoV-2 infected human cells

24. Espino, J.A., King, C.D., Jones, L.M. and Robinson, R.A., 2020. In Vivo Fast Photochemical Oxidation of Proteins Using Enhanced Multiplexing Proteomics. Analytical Chemistry. - Proteome Discoverer and IRS; SPS-MS3 Fusion Lumos; Photochemical oxidative footprinting in C. elegans.

25. Stepler, K.E., Mahoney, E.R., Kofler, J., Hohman, T.J., Lopez, O.L. and Robinson, R.A., 2020. Inclusion of African American/Black adults in a pilot brain proteomics study of Alzheimer's disease. Neurobiology of disease, 146, p.105129. - brain proteomics to study Alzheimer's disease

26. Schäfer, H., Beckert, B., Frese, C.K., Steinchen, W., Nuss, A.M., Beckstette, M., Hantke, I., Driller, K., Sudzinová, P., Krásný, L. and Kaever, V., 2020. The alarmones (p) ppGpp are part of the heat shock response of Bacillus subtilis. PLoS genetics, 16(3), p.e1008275. - bacterial heat stress response

27. Gupta, R., Min, C.W., Kim, S.W., Yoo, J.S., Moon, A.R., Shin, A.Y., Kwon, S.Y. and Kim, S.T., 2020. A TMT-Based Quantitative Proteome Analysis to Elucidate the TSWV Induced Signaling Cascade in Susceptible and Resistant Cultivars of Solanum lycopersicum. Plants, 9(3), p.290. - MaxQuant and IRS; MS2 Q Exactive; tomato leaf after TSWV treatment

28. da Silveira, W.A., Fazelinia, H., Rosenthal, S.B., Laiakis, E.C., Kim, M.S., Meydan, C., Kidane, Y., Rathi, K.S., Smith, S.M., Stear, B. and Ying, Y., 2020. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. Cell, 183(5), pp.1185-1201. - Multi-omic NASA GeneLab samples

29. Afshin, B., Kaushik, C., Homer, F., Hossein, F., Valery, B., Lai, P.S.H., Saravia-Butler, A.M., Hardiman, G., Taylor, D., Galazka, J.M. and Costes, S.V., 2019. Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. Scientific Reports (Nature Publisher Group), 9(1). - MaxQuant and IRS; ; mouse livers

30. Van de Walle, P., Geens, E., Baggerman, G., José Naranjo-Galindo, F., Askjaer, P., Schoofs, L. and Temmerman, L., 2019. CEH-60/PBX regulates vitellogenesis and cuticle permeability through intestinal interaction with UNC-62/MEIS in Caenorhabditis elegans. PLoS biology, 17(11), p.e3000499. - MaxQuant and IRS; CID/HCD Orbitrap Elite; C. elegans egg development

31. Wu, M., McCain, J.S.P., Rowland, E., Middag, R., Sandgren, M., Allen, A.E. and Bertrand, E.M., 2019. Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators. Nature communications, 10(1), pp.1-10. - Proteome Discoverer/SEQUEST and IRS; MS2 Orbitrap Velos Pro; Prymnesiophyceae (algae) mineral deficiencies

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Phillip Wilmarth
OHUS PSR Core
July 7, 2020